CDX2.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX2.H12INVITRO.0.PS.A
Gene (human)	CDX2 (GeneCards)
Gene synonyms (human)	CDX3
Gene (mouse)	Cdx2
Gene synonyms (mouse)	Cdx-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	nKTTATKRbn
GC content	32.83%
Information content (bits; total / per base)	9.155 / 0.916
Data sources	ChIP-Seq + HT-SELEX
Aligned words	6250

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	10 (61)	0.823	0.984	0.747	0.961	0.813	0.96	2.528	3.809	104.337	214.444
Mouse	21 (117)	0.882	0.979	0.828	0.967	0.858	0.949	2.928	3.851	142.066	319.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.809	0.762	0.72	0.69	0.641	0.632
Overall, 4 experiments	best	0.862	0.804	0.794	0.741	0.723	0.682
Methyl HT-SELEX, 1 experiments	median	0.845	0.78	0.794	0.734	0.723	0.682
Methyl HT-SELEX, 1 experiments	best	0.845	0.78	0.794	0.734	0.723	0.682
Non-Methyl HT-SELEX, 3 experiments	median	0.774	0.744	0.651	0.645	0.576	0.587
Non-Methyl HT-SELEX, 3 experiments	best	0.862	0.804	0.789	0.741	0.706	0.677

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.783	3.907	0.291	0.197

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	CDX {3.1.1.9} (TFClass)
TFClass ID	TFClass: 3.1.1.9.2
HGNC	HGNC:1806
MGI	MGI:88361
EntrezGene (human)	GeneID:1045 (SSTAR profile)
EntrezGene (mouse)	GeneID:12591 (SSTAR profile)
UniProt ID (human)	CDX2_HUMAN
UniProt ID (mouse)	CDX2_MOUSE
UniProt AC (human)	Q99626 (TFClass)
UniProt AC (mouse)	P43241 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 21 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CDX2.H12INVITRO.0.PS.A.pcm
PWM	CDX2.H12INVITRO.0.PS.A.pwm
PFM	CDX2.H12INVITRO.0.PS.A.pfm
Alignment	CDX2.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	CDX2.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	CDX2.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	CDX2.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	CDX2.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	CDX2.H12INVITRO.0.PS.A_homer_format_0.001.txt CDX2.H12INVITRO.0.PS.A_homer_format_0.0005.txt CDX2.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1272.75	1768.75	1816.75	1391.75
02	484.75	166.75	888.75	4709.75
03	0.0	0.0	0.0	6250.0
04	663.0	0.0	53.0	5534.0
05	6250.0	0.0	0.0	0.0
06	0.0	1155.0	34.0	5061.0
07	323.0	180.0	3493.0	2254.0
08	3005.0	310.0	2818.0	117.0
09	557.0	3175.0	1081.0	1437.0
10	1271.75	1774.75	1802.75	1400.75

PFM

	A	C	G	T
01	0.204	0.283	0.291	0.223
02	0.078	0.027	0.142	0.754
03	0.0	0.0	0.0	1.0
04	0.106	0.0	0.008	0.885
05	1.0	0.0	0.0	0.0
06	0.0	0.185	0.005	0.81
07	0.052	0.029	0.559	0.361
08	0.481	0.05	0.451	0.019
09	0.089	0.508	0.173	0.23
10	0.203	0.284	0.288	0.224

PWM

	A	C	G	T
01	-0.205	0.124	0.151	-0.116
02	-1.167	-2.226	-0.563	1.102
03	-6.574	-6.574	-6.574	1.385
04	-0.855	-6.574	-3.345	1.264
05	1.385	-6.574	-6.574	-6.574
06	-6.574	-0.302	-3.767	1.174
07	-1.571	-2.15	0.804	0.366
08	0.653	-1.612	0.589	-2.575
09	-1.029	0.708	-0.368	-0.084
10	-0.206	0.127	0.143	-0.109

Standard thresholds

P-value	Threshold
0.001	5.185525
0.0005	6.00421
0.0001	7.43888